Downlad stable versions of LFPy here:
Or, download the development version of LFPy using subversion into a local folder:
svn checkout http://bebiservice.umb.no/svn-public/LFPy-release
The development code is then found under “trunk/”, and different numbered releases under “tags/”.
To browse the source codes online, see http://bebiservice.umb.no/projects-public/LFPy-release/browser.
To install LFPy you will need the following:
Python, seems to work fine with recent python since 2.6.x (2.6.6 or newer recommended), 2.7.x works fine. Not tested with Python 3.x.
Python modules numpy, scipy, matplotlib
NEURON compiled as a Python module, so the following should execute without error in Python console:
import neuron
neuron.test()
If this step fails, see the next section.
LFPy was tested to work with NEURON 7.2 and the 7.3 development branch, we had some issues with a precompiled version of NEURON 7.1.
Cython (C-extensions for python) to speed up simulations of extracellular fields. Tested with version > 1.4., and known to fail with version 1.1.
There are few options to install LFPy:
From the Python Package Index with only local access using pip
pip install --user LFPy
as sudoer:
sudo pip install LFPy
From the Python Package Index with only local access using easy_install
easy_install --user LFPy
as sudoer:
sudo easy_install LFPy
From source:
tar -xzf LFPy-x.x.tar.gz
cd LFPy-x.x
(sudo) python setup.py install (--user)
Development version from subversion repository:
svn checkout http://bebiservice.umb.no/svn-public/LFPy-release/
cd LFPy-release/trunk
(sudo) python setup.py install (--user)
If you only want to have LFPy in one place, you can add this working folder to your $PYTHONPATH, and just compile the Cython extensions;
python setup.py build_ext -i
In a fresh python-session you should now be able to:
import LFPy
Some users have difficulties install NEURON as a Python module, depending on their platform. We will provide some explanations here, and otherwise direct to the NEURON download pages; http://www.neuron.yale.edu/neuron/download and http://www.neuron.yale.edu/neuron/download/getstd. The NEURON forums are also a useful resource for installation problems.
The instructions below show how to meet all the requirements starting from a clean Ubuntu 10.4 for the installation of NEURON from the development branch.
Start by installing the required packages
sudo apt-get install mercurial autoconf libtool
sudo apt-get install libxext-dev libncurses-dev
sudo apt-get install bison flex
sudo apt-get install python-dev python-numpy python-scipy python-matplotlib
sudo apt-get install ipython
The cython version provided in Ubuntu 10.4LTS is out of date, compile a more recent version yourself. Download Cython (Cython-0.15.1.tar.gz, or newer) from Cython.org, unpack and install;
sudo python setup.py install
Now get the source code of NEURON using mercurial
cd $HOME
mkdir neuron
cd neuron
hg clone http://www.neuron.yale.edu/hg/neuron/iv
hg clone http://www.neuron.yale.edu/hg/neuron/nrn
Compile and install InterViews
cd iv
sh build.sh
./configure --prefix=`pwd`
make
make install
Compile and install NEURON
cd ../nrn
sh build.sh
./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-nrnpython=/usr/bin/python
make
make install
Install NEURON as a Python module
cd src/nrnpython/
sudo python setup.py install
(or python setup.py install --user if you want to install the Python package in your home folder).
Now you should be able to import neuron from Python console and run a small test with success;
cd $HOME
ipython
import neuron
neuron.test()
You might want to add the folder with NEURON executables to your PATH, so that you can easily compile NEURON mechanisms using nrnivmodl
export PATH=$PATH:$HOME/neuron/nrn/x86_64/bin
Most of the development work and testing of LFPy has been done on Max OS X 10.6.* Snow Leopard and 10.7.* Lion. Our preferred way of building Python has been through MacPorts; http://www.macports.org. Here is an step-by-step explanation on how to compile NEURON agains that installation of Python.
To start using MacPorts, follow the instructions on http://www.macports.org/install.php.
Building a python 2.7 environment using MacPorts issue in Terminal:
sudo port install python27 py27-ipython py27-numpy py27-matplotlib py27-scipy py27-cython
Make the installed Python and IPython default:
sudo port select --set python python27
sudo port select --set ipython ipython27
Install the necessary packages for cloning into repository and compiling NEURON:
sudo port install automake autoconf libtool libxext xorg-libXext ncurses mercurial bison flex
Install NEURON from the bleeding edge source code. The following recipe assumes a 64 bit build of NEURON and Python on OSX 10.7 Lion, so change “x86_64-apple-darwin10.7.0” throughout to facilitate your system accordingly;
#create a directory in home directory
cd $HOME
mkdir nrn64
cd nrn64
#creating directories
sudo mkdir /Applications/NEURON-7.3
sudo mkdir /Applications/NEURON-7.3/iv
sudo mkdir /Applications/NEURON-7.3/nrn
#Downloading bleeding edge source code
hg clone http://www.neuron.yale.edu/hg/neuron/iv
hg clone http://www.neuron.yale.edu/hg/neuron/nrn
cd iv
#compiling and installing IV under folder /Applications/nrn7.3
sh build.sh
./configure --prefix=/Applications/NEURON-7.3/iv \
--build=x86_64-apple-darwin10.7.0 --host=x86_64-apple-darwin10.7.0
make
sudo make install
#Building NEURON with InterViews, you may have to alter the path --with-nrnpython=/python-path
cd $HOME/nrn64/nrn
sh build.sh
./configure --prefix=/Applications/NEURON-7.3/nrn --with-iv=/Applications/NEURON-7.3/iv \
--with-x --x-includes=/usr/X11/include/ --x-libraries=/usr/X11/lib/ \
--with-nrnpython=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python \
--host=x86_64-apple-darwin10.7.0 --build=x86_64-apple-darwin10.7.0
make
sudo make install
sudo make install after_install
#You should now have a working NEURON application under Applications. Small test;
#sudo /Applications/NEURON-7.3/nrn/x86_64/bin/neurondemo
#Final step is to install neuron as a python module
cd src/nrnpython
sudo python setup.py install
If you prefer to use Enthough Python distribution, see this forum post: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=2&t=2191
There is a package PyNEURON on the Python package index, PiPy: http://pypi.python.org/pypi/PyNEURON/ and a corresponding forum thread on the NEURON homepage here; http://www.neuron.yale.edu/phpBB/viewtopic.php?f=2&t=2501
If you have pip installed, try:
pip install PyNEURON